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Yorodumi- PDB-3o92: High resolution crystal structures of Streptococcus pneumoniae ni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o92 | ||||||
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Title | High resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into catalytic mechanism and inhibition by aldehydes | ||||||
Components | nicotinamidase | ||||||
Keywords | HYDROLASE / Nicotinamidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | French, J.B. / Cen, Y. / Sauve, A.A. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: High-resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into the catalytic mechanism and inhibition by aldehydes . Authors: French, J.B. / Cen, Y. / Sauve, A.A. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o92.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o92.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 3o92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o92_validation.pdf.gz | 469.8 KB | Display | wwPDB validaton report |
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Full document | 3o92_full_validation.pdf.gz | 475.1 KB | Display | |
Data in XML | 3o92_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 3o92_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/3o92 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o92 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23762.582 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1583 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97PM2, UniProt: A0A0H2UR34*PLUS #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 18-22% PEG 3350, 0.2-0.3M NaCl, 0.2M Sodium Malonate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 67200 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rsym value: 0.098 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.353 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.078 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.327 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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